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Builds a NicheNet signaling network

Source: R/nichenet.R
nichenet_signaling_network.Rd

Builds signaling network prior knowledge for NicheNet using multiple resources.

Usage

nichenet_signaling_network(
  omnipath = list(),
  pathwaycommons = list(),
  harmonizome = list(),
  vinayagam = list(),
  cpdb = list(),
  evex = list(),
  inbiomap = list(),
  only_omnipath = FALSE
)

Arguments

omnipath

List with paramaters to be passed to nichenet_signaling_network_omnipath.

pathwaycommons

List with paramaters to be passed to nichenet_signaling_network_pathwaycommons.

harmonizome

List with paramaters to be passed to nichenet_signaling_network_harmonizome.

vinayagam

List with paramaters to be passed to nichenet_signaling_network_vinayagam.

cpdb

List with paramaters to be passed to nichenet_signaling_network_cpdb.

evex

List with paramaters to be passed to nichenet_signaling_network_evex.

inbiomap

List with paramaters to be passed to nichenet_signaling_network_inbiomap.

only_omnipath

Logical: a shortcut to use only OmniPath as network resource.

Value

A network data frame (tibble) with signaling interactions suitable for use with NicheNet.

See also

Examples

# load everything with the default parameters:
# we don't load inBio Map due to the - hopefully
# temporary - issues of their server
sig_network <- nichenet_signaling_network(inbiomap = NULL, cpdb = NULL)
#> Error in map2(., names(.), function(args, resource) {    args$quality_filter_param <- if (network_type == "lr" &&         resource == "OmniPath")         quality_filter_param    else NULL    resource %T>% {        log_info("Loading resource `%s`.", .)    } %>% sprintf("nichenet_%s_network_%s", network_type, .) %>%         get() %>% do.call(args)}): ℹ In index: 4.
#> ℹ With name: vinayagam.
#> Caused by error:
#> ! HTTP 403

# override parameters for some resources:
sig_network <- nichenet_signaling_network(
    omnipath = list(resources = c('SIGNOR', 'SignaLink3', 'SPIKE')),
    pathwaycommons = NULL,
    harmonizome = list(datasets = c('phosphositeplus', 'depod')),
    # we can not include this in everyday tests as it takes too long:
    # cpdb = list(complex_max_size = 1, min_score = .98),
    cpdb = NULL,
    evex = list(min_confidence = 1.5),
    inbiomap = NULL
)
#> Error in map2(., names(.), function(args, resource) {    args$quality_filter_param <- if (network_type == "lr" &&         resource == "OmniPath")         quality_filter_param    else NULL    resource %T>% {        log_info("Loading resource `%s`.", .)    } %>% sprintf("nichenet_%s_network_%s", network_type, .) %>%         get() %>% do.call(args)}): ℹ In index: 3.
#> ℹ With name: vinayagam.
#> Caused by error:
#> ! HTTP 403

# use only OmniPath:
sig_network_omnipath <- nichenet_signaling_network(only_omnipath = TRUE)